Related papers: smFISH_batchRun: A smFISH image processing tool fo…
Subcellular RNA localization is a critical mechanism for the spatial control of gene expression. Its mechanism and precise functional role is not yet very well understood. Single Molecule Fluorescence in Situ Hybridization (smFISH) images…
Staphylococcus aureus is an important pathogen, giving rise to antimicrobial resistance in cell strains such as Methicillin Resistant S. aureus (MRSA). Here we report an image analysis framework for automated detection and image…
Single-cell RNA sequencing (scRNA-seq) technology enables systematic delineation of cellular states and interactions, providing crucial insights into cellular heterogeneity. Building on this potential, numerous computational methods have…
Multicolor in situ hybridization (mFISH) is a karyotyping technique used to detect major chromosomal alterations using fluorescent probes and imaging techniques. Manual interpretation of mFISH images is a time consuming step that can be…
As camera pixel arrays have grown larger and faster, and optical microscopy techniques ever more refined, there has been an explosion in the quantity of data acquired during routine light microcopy. At the single-molecule level, analysis…
Single-cell RNA-sequencing (scRNA-seq) stands as a powerful tool for deciphering cellular heterogeneity and exploring gene expression profiles at high resolution. However, its high cost renders it impractical for extensive sample cohorts…
Nanoscale secondary ion mass spectrometry (nanoSIMS) and fluorescence in situ hybridization (FISH) microscopy provide high-resolution, multimodal image representations of the identity and cell activity respectively of targeted microbial…
RNA structure determination is essential for understanding its biological functions. However, the reconstruction process often faces challenges, such as atomic clashes, which can lead to inaccurate models. To address these challenges, we…
A critical challenge in single-cell RNA sequencing (scRNA-seq) integration is resolving the tension between eliminating batch effects and maintaining biological fidelity. While recent evidence indicates that batch effects manifest…
Single-Cell RNA sequencing (scRNA-seq) measurements have facilitated genome-scale transcriptomic profiling of individual cells, with the hope of deconvolving cellular dynamic changes in corresponding cell sub-populations to better…
The rapid and accurate detection of biochemical compositions in fish is a crucial real-world task that facilitates optimal utilization and extraction of high-value products in the seafood industry. Raman spectroscopy provides a promising…
The quantitative analysis of cellular membranes helps understanding developmental processes at the cellular level. Particularly 3D microscopic image data offers valuable insights into cell dynamics, but error-free automatic segmentation…
Automated fish documentation processes are in the near future expected to play an essential role in sustainable fisheries management and for addressing challenges of overfishing. In this paper, we present a novel and publicly available…
Motivation: Illumina DNA sequencing is now the predominant source of raw genomic data, and data volumes are growing rapidly. Bioinformatic analysis pipelines are having trouble keeping pace. A common bottleneck in such pipelines is the…
Single-cell RNA sequencing (scRNA-seq) has transformed our ability to explore biological systems. Nevertheless, proficient expertise is essential for handling and interpreting the data. In this paper, we present scX, an R package built on…
FISH is a fast and simple ideal magneto-hydrodynamics code that scales to ~10 000 processes for a Cartesian computational domain of ~1000^3 cells. The simplicity of FISH has been achieved by the rigorous application of the operator…
Since its selection as the method of the year in 2013, single-cell technologies have become mature enough to provide answers to complex research questions. With the growth of single-cell profiling technologies, there has also been a…
Single-cell RNA sequencing (scRNA-seq) reveals cell heterogeneity, with cell clustering playing a key role in identifying cell types and marker genes. Recent advances, especially graph neural networks (GNNs)-based methods, have…
The expanding adoption of digital pathology has enabled the curation of large repositories of histology whole slide images (WSIs), which contain a wealth of information. Similar pathology image search offers the opportunity to comb through…
RNA-seq has rapidly become the de facto technique to measure gene expression. However, the time required for analysis has not kept up with the pace of data generation. Here we introduce Sailfish, a novel computational method for quantifying…